


Re Write Series

by Grace_in_the_Stars



Series: Star Trek Voyager - Re Write Series [1]
Category: Star Trek: Voyager
Genre: Action/Adventure, Angst and Romance, Canon Rewrite, Deviates From Canon, Episode: s01e01 Caretaker, F/M, Multi-pairings explored
Language: English
Status: Completed
Published: 2018-04-28
Updated: 2018-10-21
Packaged: 2019-04-29 04:13:56
Rating: General Audiences
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 5
Words: 3,680
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/14464770
Author URL: https://archiveofourown.org/users/Grace_in_the_Stars/pseuds/Grace_in_the_Stars
Summary: This is a kind of preview fic if you like to a series rewrite that has been in my Voyager addled brain forever. If you guys like, I will post more. I honestly have like 9 seasons in me. I am not kidding.  So here goesIn this preview to the series we meet Captain Kathryn Janeway, as she is given her assignment to capture Chakotay's maquis crew.





	1. A Janeway Belongs in the Stars

**Author's Note:**

> DISCLAIMER: Star Trek: Voyager and all its characters belong to Paramount Pictures; no infringement of copyright is intended. 
> 
> Please note I am Scottish, so American writers may notice changes with some words etc. I try to stick to the lingo the characters would say, but if I stray to British spelling please forgive me.
> 
> Chapter 1 is just an intro , the rest will be longer as we meet Voyager and her crew and the real mission begins. 
> 
> Kathryn Janeway's back story will diverge from canon slightly as will most of the regular cast that are familiar to us. Don't worry they will still be the crew we love.

 

 ~~~~Captain Kathryn Janeway walked into Starfleet Command at 0900 hours. She was expecting to meet with Admiral Haze regarding a new mission, but he was not in his office, instead she came face to face with Captain Picard, Commanders Sisko and Riker and Admiral Paris.

 

“Sir what’s going on?’’  
Owen Paris smiled at his former protégé and and said, “have a seat Captain, this is going to take a while.” Kathryn sighed, she knew this was going to be a bad day.

 

..........

Five hours later, Kathryn left command and made her way home. She had to get organised for this mission.

 

She was still in shock! She was being sent to bring in a maquis rebel, named Chakotay. He was the leader of a cell doing some serious damage to the Cardassians. He had a motto, he did not go after Starfleet ships. He was only after Cardassians. Kathryn thought this was noble but would not voice this to her superiors.

She was further shocked to learn that a section 31 operative was uncover on-board Chakotay’s ship and she was to bring him in for interrogation. It seemed the Federation had enemies everywhere these days, she did not sign up to fight wars, but to explore.

She was a born explorer, like her parents. Both Starfleet officers, known to most in the Federation. Her mother even gave birth to Kathryn while on assignment in the Neutral Zone.She grew up hearing, ‘A Janeway’s belongs in the stars’, so she followed her dreams all the way to Starfleet.

She had worked her way up from the science track and then the command track. She wanted to do her duty. Be her best. Make her parents proud. Now instead of exploring on her brand-new ship, the USS Voyager, she was ferrying diplomats and hunting down people who were considered enemies to the Federation!

 

Kathryn wondered what had become of her precious Starfleet. She shook her head and forced herself to remember the oath she had taken. She would do her duty, she would find the Val Jean and the operative and bring them all home again. It was a three-week mission max.

.......

  
After getting her belongings shipped to Voyager and informing her First Officer of the new mission, Kathryn had one more stop to make.

“Tom Paris?” she barked at the blonde-haired man sweating as he worked away at SF’s finest penal colony.

  
“Kate? Is that. Oh, you are a sight for sore eyes and its Captain Kate now, I see.” he grinned, asaKathryn gave him her trade mark smirk, “Listen up Tom, I can get you out of here, but first you are going to do a little job for us.’’

  
Tom looked at her and shook his head. “No way. For you maybe, for the Federation, no way. Besides I have it made here. I’m good. Nice to see you.’’

  
Kathryn grabbed his arm as he made to leave. “Tom, he doesn’t blame you. Not anymore.’’

  
Tom laughed “He should never have blamed me! My brother died, and my dad blamed me. He was my big brother Kate, I looked up to him. I loved him.”

  
“So, did I, Tom. I was going to marry him.’’ Kathryn held his stare and they walked in silence until Tom asked, “What’s the mission then?’’.

Kathryn Janeway smiled.


	2. Not A Peaceful Man

**Summary for the Chapter:**

> Chakotay rallies his people for war, unaware of the deception surrounding him.

**Notes for the Chapter:**

> Thank you to Klugtiger for the beta. You have been a tremendous help. 
> 
> See disclaimer in chapter one.

B’Elanna Torres was not happy. She was stuck with an ancient engine and a boss who expected her to come up with miracles. Life as a Maquis was no walk in the park, she knew that, but she never considered it would be this hard. She was not impressed with her options, but as this was a trading post on a seedy backwater planet, she had to make do. B’Elanna had gotten used to doing that in her life.

“That’s enough Dalby. We are gonna need to get these supplies back to the Val Jean ASAP otherwise the old man will have my ass.’’

“You wish he would have your ass.’’ Dalby mocked.

“Shut it P’tak, get a move on okay?” She glared at him; she picked up a crate of repair tools and stalked off with Dalby trailing behind.

……

Captain Chakotay of the Maquis arrived on the small bridge of the Val Jean, his ship, to find his good friends Michael Ayala and Kurt Bendarra waiting.

“Ready to get underway Old Man?” Ayala quipped, watching as Chakotay sat in his command chair, the tattoo on his forehead creasing as he frowned.

“Is Torres back yet? We need those supplies.’’

“She just got here, so we should head out, never know when the Cardies will turn up!’’ Ayala stated.

“Or the Feds!’’ Bendarra pointed out.

Chakotay let them talk as they prepared the ship for departure. His plan was to take his ship and crew into the Badlands and hide out from the Cardassians. Lately his crew was getting noticed as they were doing some serious damage to the Cardies and the precious Federation Alliance.

Chakotay smiled, it felt good knowing they had dealt a blow to the Alliance that doomed his people, his family. He shook his head as images of his father dying fighting a Cardassian soldier, after a blow to the head. His sister and mother were brutally violated and murdered, and their bodies left to rot. Chakotay shook his head and pushed the morbid thoughts aside and stood up motioning to Mike Ayala.

“Ayala put me on ship wide audio. Alright people, listen up. We are leaving this trading post and heading to the Badlands. Over the past months we have dealt a massive blow to both the Cardassians and the Federation Alliance!’’ Chakotay paused as his crew roared and cheered.

“Now it’s time to retreat, get our ship repaired, and come back fighting harder than ever. I promise you all, we will not rest until we end the brutality of the Cardassians. Our numbers are growing, and we have taken down several Cardassian outposts. We will weaken them. They Came to our lands and murdered our people. We will have blood!’’

The Maquis leader sat back down as Bendarra took the Val Jean into the Badlands.

 

……

“Nice speech Old Man.’’ Purred a female voice as Chakotay sat on his bunk hours later, clad in sweatpants and nothing else.

She stood before him, her brown eyes looking into his. She could see the determination in his eyes.

“It was the truth. I’m only retreating to ensure we come back stronger, and since when do you call me ‘Old man?’’’ He smirked at his lover.

“Oh, you don’t like it? I thought you might.’’ She grinned looking down into his lap.

“Oh, you know what I like, you vixen.’’ He laughed, pulling her down to straddle his lap.

“Yes, I do, and I intend to take full advantage of that knowledge! Right now.’’ Seska whispered in his ear as she pushed him down onto the bunk.

 

......

 

He watched them as they began to kiss and caress each other and then turned off the monitor, not really wanting to see a Cardassian getting it on, even if she was disguised as a Bajoran.

His job was clear now, he had to get word to his contact. If what he suspected was the case, Chakotay was going to lead more of his people to war. The Val Jean captain was not a peaceful man, he wanted revenge for the murder of his people, but there was another side to him.

Chakotay was once a Starfleet Officer and would have been made captain before he left. Chakotay had become an asset to the Maquis, but he did not consider the ‘Fleeters the enemy and would not allow his crew to attack any Starfleet vessel unless they attacked first, and even then, he refused to take action that would condemn his former comrades to death.

As smart and headstrong as the Maquis Captain was, he had no idea that the woman currently in his bed was a spy for the people who slaughtered his family. Seska was a problem, but one he could deal with, he was confident of that. Now it was time to inform Section 31 of his findings. Chakotay had to be stopped, whatever the cost.


	3. First Day

**Summary for the Chapter:**

> Kathryn Janeway prepares for her mission as Paris and another new recruit arrives on board.

**Notes for the Chapter:**

> Thank you to Caladeniablue for being my beta. I learned a lot from her.
> 
> Please note that Janeway’s partner in the story is not Mark. Again her backstory will differ from canon slightly. This will unravel as the story progresses.
> 
> I hope you all enjoy. Feedback would be much appreciated.

“We still have to set a date, Kathryn. You know I’d wait forever, love, but everyone from my grandma to the brass keeps asking me about when we plan to get married.’’ Marcus Kent grinned through the viewer.

  
“I know, Marcus, I know. My mother is the same, trust me. When I get back we’ll set a date. Deal?’’

  
“How can I resist you?” he said smiling. Then his voice dipped “Be careful with this mission. Those Maquis are ruthless.”

  
”It's only a three-week mission—bring in the Maquis and come home,’’ Kathryn said, unable to tell him that she had a secondary mission. She told herself as a fellow captain he would understand.

  
The door to her ready room chimed.

  
“Marcus, I have to go. See you in three weeks.”

“You better. Love you.’’ He smiled.  
“You too.’’ She kissed her fingers and placed on the screen before signing off and standing to greet her guests.

  
“Captain Janeway, I thought you would like to meet our new Chief of Security, lieutenant Tuvok,’’ Commander John Cavit stood with his usual dour expression next to the Vulcan officer.

  
“Hello, old friend,’’ Kathryn said, secretly enjoying the surprised expression on Cavit's face.

  
“It is pleasing to see you again, Kath— I mean, Captain Janeway,’’ Tuvok replied.

  
Cavit was looking back and forth so Kathryn decided to explain.

  
“Tuvok served with both my parents many years ago. He’s an old family friend. I've known him since I was a girl but it's been some time since we met.’’

  
“20 years, 4 months, 3 days to be exact.’’ Tuvok corrected.

  
“Right, well, I guess there was no need for the introductions then,’’ Cavit responded in a testy tone.

  
“Thank you, Commander. You are dismissed. Oh, and when Tom Paris arrives, please send him here.’’ She smiled and ignored Cavit’s annoyance as he left, before turning her attention back to Tuvok.

 

 

Tal Celes was excited. Yes, she was about to embark on her mission as a crewman of the USS Voyager. Yes, she suspected her placement was to make a show of having another Bajoran in Starfleet and yes, she could have aced her exams better, but here she was. Celes was excited, but she was still nervous.

  
She walked into the mess hall to instant chatter. Celes noticed a handsome young man with raven black hair, an Ensign talking to two identical human females. Celes decided she should make some friends, but who? Everyone appeared to be sitting in groups talking and laughing.

  
“Hi there.’’  
Celes whipped around to find a blond human male with blue eyes and a cheeky grin.

  
“First-day nerves huh. It’s like being back at the Academy. Who are the cool cadets? Who are the losers?‘’ he rambled on.

  
“Who are you?’’ She could see no rank but he was no crewman, not by the way he stood with the air of confidence of a seasoned officer.

  
“Tom Paris.’’ He held out his hand to her.  
“Celes. No, Tal. I mean my name is Tal Celes.’’ She shook his hand.

  
“It’s cool. I'm familiar with Bajoran name customs,’’ Tom told her.

  
Although it was refreshing to find someone who understood Bajoran names, this guy fancied himself for sure. She made a mental note to stay away. Guys like him usually wanted sex and she was here to explore stellar phenomena, not interspecies mating customs.

  
“Look, if I'm bothering you, please say. I’m new too and so far today the only people not to scoff at me have been the Captain and that new ensign.’’ He nodded to the young man she'd noticed earlier.

  
“Why would people scoff at you? I mean, you are rather annoying, but I am sure guys like you can charm people, so what’s the problem?’’ Celes asked, wondering when her mouth had detached from her brain.

  
“Wow, you and Ensign Kim seem to be the only ones in the whole ship who don't know who I am. Well, ask around and then you'll see.’’

  
“I don’t make judgements based on other people’s remarks, Mr Paris, but I can’t say you are endearing me to your side.’’

  
“Trust me, you don’t want me on your side.’’ Tom frowned when two older officers, one medical and the other she recognised as the first officer began talking to the Ensign.

  
“I’ll see you around, Tal.’’ Paris winked at her and walked over to his friend as the other two men gave him a look of disdain.

  
”Paris, the Captain wants to see you.” Tal overheard the first officer say to Tom and she caught a look of hatred in the older man's eyes.

  
”Yes, Sir.” Paris mocked saluted and walked out.

  
“This mission is going to be fun”, she thought.

  
Yes, Tal Celes was nervous.

 

 

  
“Section 31 has an agent on Chakotay's crew? I assume you don't just want to bring them in, then?” Tom stood in the Ready Room, facing his Captain.

  
“It's my secondary mission, after apprehending the Maquis. You are the only one besides myself and Tuvok who knows about it,” Kathryn said.

  
“Not even your First Officer?” Tom smugly crossed his arms. Kathryn knew Tom obviously found the man to be rude and pretty arrogant. So did she.

  
“This is a need-to-know only mission. You need to know. I do hope I can trust you not to reveal this fact to anybody else on this ship.” She rose from her seat.

  
“Of course you can. You have my word.” Tom replied sincerely.

  
Kathryn Janeway knew this mission was going to be dangerous but her duty was clear. She trusted Tuvok. After all, he had always been part of her life. He was her family. As for her old friend Tom… Once upon a time she would have taken him at his word.

  
“ Don't let me regret this, Tom,” she told him as they left her ready room and headed to the bridge.

 


	4. The Hand We Are Dealt

**Summary for the Chapter:**

> Scenes will differ from canon. Janeway's backstory regards to her parents will be different from canon but still recognisable. I wanted to give Gretchen Janeway more of a story and intend to do this if I write more. 
> 
> Not beta read as I wrote this on a train and was excited to post. I hope you enjoy this. Final chapter is done and will be up soon.

”So Chakotay, what do you say? Do we have a deal?” Kathryn asked the Maquis Captain.

Chakotay took a deep breath as the Starfleet Captain handed out her hand to him. His once enemy was proposing the impossible, but after everything that had occurred since they were brought to this strange quadrant, he believed she might do it. He just wasn't about to bend the knee to Starfleet again but he wanted the same as her. To get his people home and after all whatever choice was there.

…….

“You are speaking to a member of my crew. I expect you to treat him with the same respect you would have me treat a member of yours.” Janeway stood toe to toe with the Maquis Captain.

Chakotay saw no fear in the Starfleet Captain's eyes and as he nodded to Ayala to drop weapons and Paris looked at Janeway gratefully, Chakotay realized who she was and cursed inwardly. 

”Ayala where are your manners? Don't you know we are in the presence of Starfleet royalty here? Bow,before the Queen.”

Kathryn shook her head but remained silent.

”I suggest if we want to find our missing crewmen we work together. Can you do that Captain Chakotay?”

Chakotay relented as she appeared unfazed by his comments, looking him in the eye, chin raised and hands on hips. His anger at finding that traitor on board would have to wait. 

”Lead the way Starfleet.”

Chakotay explained to Ayala that Janeway was the daughter of two well known fleeters. Her parents were once prominent officers which meant only one thing as far as Chakotay was concerned.

“She's a fleet brat Ayala. Starfleet is in her blood. That's why they sent her!” Chakotay had seethed.

 

As the two crews worked together to find Kim and Torres, they met a strange fellow called Neelix. He called himself a scavenger and claimed to know about other ships being brought to the quadrant. Neelix offered to help for a price, Janeway had Tuvok meet him and provide the strange fellow with supplies for his ship.

“I am happy to help you of course but I will not get involved with those pirates, no, no, not me. I have remained alive this long because of my smarts.” Neelix had implored to both captains. 

Neelix told them all about the pirates that ran the region. They were called Kazon and stole ships and killed the crew on board. All this to expand their power. As they escaped from the Kazon, helping to free a captured slave called Kes, and were reunited with their people on the Kes's homeworld.Kes explained her people had been protected by the Caretaker, but she had left to explore and got captured. 

Chakotay had then ordered his crew to beam over to Voyager. Seska had told him it was a stupid move and he was just handing them to Janeway. 

"Why not leave the Feds to it and make our way back?" She begged her lover.

Chakotay locked eyes with Ayala before his friend grabbed a hold of Seska and left Chakotay to sacrifice the Val Jean. 

……. 

 

”I guess you got yourself a new XO Starfleet. ” He accepted her hand and sealed his fate. 

”Time to tell our crew Commander. ” Kathryn smiled trying out his new title.

”This should be fun.” he shot back as they left her ready room and headed to the Cargo Bay. 

……….

Kathryn knew that they had to make this work. It was a tactical move on both their parts. They had learned about the Caretaker and understood he had a motive for bringing them to the Delta Quadrant. They just didn't know why. The entity died before he could send them home and with him, the power. They had tried to understand more about the array but its existence meant the Kazon could gain more power and Kathryn was faced with only one choice.

“Any chance we can destroy that thing from our end Tuvok?” 

“Negative Captain.” The Vulcan explained.

So she had made a decision that sealed all their fates to Voyager. The look she got from Torres told her everything she needed to know.

………

“You will need to set an example. Wear the uniform. They will follow your lead Commander.” 

“Yes but you want them to follow your lead Captain, and to do that, you need their respect.” Chakotay smiled sincerely.

She usually could read people but this man seemed to be a contradiction. He claimed to be angry at the Federation but he followed her lead. The woman he had called a brat when he thought she wasn't listening. He still supported her decision and he could have agreed with Torres but instead shut her down.

“That is going to take time. I don't expect an overnight change.” She explained. 

“Some maybe angry at your choice but they know deep down, as a Maquis, it was the right thing to do.”

Relieved, she smiled back as she joined him to face their crew. They had no choice, but to deal with the hand they had been dealt.


	5. Two Faces

**Summary for the Chapter:**

> So here is the final installment of my Rewrite Series. This was planned as an intro or an alternative Caretaker if you prefer.
> 
> I hope you enjoy.

Michael Ayala returned to his new quarters and let out a breath. So this was it. This was the price of the life he choose. He had no belongings to unpack just the small device in his pocket. He took out the small listening device and threw it across the room.

“Damn!”

His mission was screwed! He he was an agent of Section 31 with no way out. He was stuck on a Starfleet ship as Michael Ayala. He had no way to contact his superiors. He could of course continue his mission but what if they were out here for good. 

He started pacing back and forth. His analytical mind trying to figure this out.

He had dedicated his life to the agency. He had walked away from his family, his career and his lover and all for nothing. How could he do this now?

If Chakotay found out the truth, he’d kill him. He was certain of that. That was problem one. Problem two was Seska. He knew who she was and she too was now without her mission. What would her next move be? He couldn’t expose her without exposing himself.

Sighing Ayala picked up the device and considered problem three.

”Kathryn Janeway. It had to be you they sent! Why?”

She had made an alliance with the Maquis, that proved to him that she could think outside the box. Just like her father. Ayala cursed as he remembered Edward Janeway and then other memories flooded back.

Memories of a young man with ideals and wanting to save the galaxy, a man who fell in love with a woman who brought out the best in him.

A man that loved competing with his brother for their father’s approval. Justin Tighe Paris. A man who died leaving the people behind devastated.

“Fuck”, he cursed. 

He hadn’t allowed himself to remember Justin in years because when he did the guilt set in. He couldn’t bare it. When he thought of Justin, he thought about her and that led down a dangerous path. He had made his choices. He had to live with it. He would continue to play the part of the Maquis solider.

He’d stay silent and become part of the background. If he did what he was trained to do, no one would know. 

He shook his head and knew he had made his choices a long time ago. He had to find a way to make this work and live with himself in the process.

Chakotay would never know his best friend was a liar, Seska that she wasn’t as cunning as she thought, Tom Paris that his brother was alive and bore a new face and Janeway would never know that her former lover was so close. Michael Ayala would take this secret to his death.


End file.
